ArticleThe Journal of chemical physics2018
A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes.
Article in The Journal of chemical physics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Determining Pathways of Minimum Work: Simple Examples.Molecular physics · 2025Article
- Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers.Journal of chemical information and modeling · 2025Article
- Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir.The Journal of chemical physics · 2024Article
- Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions.Journal of chemical information and modeling · 2024Article
- Configurational Sampling of All-Atom Solvated Membranes Using Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations.The journal of physical chemistry letters · 2024Article
- The Structures of Heterogeneous Membranes and Their Interactions with an Anticancer Peptide: A Molecular Dynamics Study.Life (Basel, Switzerland) · 2022Article
- py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.Journal of chemical theory and computation · 2022Article
- Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes.Journal of chemical information and modeling · 2022Article
- Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations.Journal of chemical theory and computation · 2021Article
- On the Consistency of the Exfoliation Free Energy of Graphenes by Molecular Simulations.International journal of molecular sciences · 2021Article
- Computer simulations of lipid regulation by molecular semigrand canonical ensembles.Biophysical journal · 2021Article
- Computer simulations of a heterogeneous membrane with enhanced sampling techniques.The Journal of chemical physics · 2020Article
- Phase Transition in a Heterogeneous Membrane: Atomically Detailed Picture.The journal of physical chemistry letters · 2020Article
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
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2 authors.
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Abstract
An algorithm to efficiently simulate multi-component fluids is proposed and illustrated. The focus is on biological membranes that are heterogeneous and challenging to investigate quantitatively. To achieve rapid equilibration of spatially inhomogeneous fluids, we mix conventional molecular dynamics simulations with alchemical trajectories. The alchemical trajectory switches the positions of randomly selected pairs of molecules and plays the role of an efficient Monte Carlo move. It assists in accomplishing rapid spatial de-correlations. Examples of phase separation and mixing are given in two-dimensional binary Lennard-Jones fluid and a DOPC-POPC membrane. The performance of the algorithm is analyzed, and tools to maximize its efficiency are provided. It is concluded that the algorithm is vastly superior to conventional molecular dynamics for the equilibrium study of biological membranes.
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